title: Peripheral T-cell lymphoma: Molecular profiling recognizes subclasses and identifies prognostic markers

status: Public on Aug 26 2021

city: Madrid

first: Laura

middle: Jiménez

last: Tomas Roca

state: Madrid

address: Avenue Reyes Catolicos

department: Pathology Department

country: Spain

institute: Research Institute Fundacion Jimenez Diaz

summary: Peripheral T-cell lymphoma (PTCL) is a clinically aggressive disease, with a poor response to therapy and a low overall survival rate of around 30% after 5 years.  We have analyzed a series of 105 cases with a diagnosis of PTCL using a customized NanoString platform that includes 208 genes associated with T-cell differentiation, oncogenes and tumor suppressor genes, deregulated pathways and stromal cell subpopulations. A comparative analysis of the various histological types of PTCL (angioimmunoblastic T-cell lymphoma, AITL; PTCL-with T follicular helper phenotype, PTCL-TFH; PTCL-not otherwise signified, PTCL-NOS) showed that specific sets of genes were associated with each of the diagnoses. These included TFH markers, cytotoxic markers and genes whose expression was a surrogate for specific cellular subpopulations, including follicular dendritic cells, mast cells and genes belonging to precise survival (NF-κB) and other pathways. Furthermore, the mutational profile was analyzed using a custom panel that targeted 62 genes in 76 cases distributed in AITL, PTCL-TFH and PTCL-NOS. The main differences between the three nodal PTCL classes involved the RHOAG17V mutations (p<0.0001), which were approximately twice as frequent in AITL (34.09%) as in PTCL-TFH (16.66%) cases, but were not detected in PTCL-NOS.  A multivariate analysis identified gene sets that allowed the series of cases to be stratified into different risk groups. This study supports and validates the current division of PTCL into these three categories, identifies sets of markers that can be used for a more precise diagnosis, and recognizes the expression of B-cell genes as an IPI-independent prognostic factor for AITL.

overall_design: 105 PTCL samples. Formalin-fixed, paraffin-embedded (FFPE) tissue sections from diagnostic biopsies were collected at the time of diagnosis before CHOP (cyclophosphamide, doxorubicin, vincristine, and prednisone), CHOP-like or CHOEP (cyclophosphamide, doxorubicin, etoposide, vincristine, and prednisone, for treating patients younger than 60 years) regimens. We analyzed 66 AITL, 21 PTCL-NOS and 18 PTCL-TFH patients.

first: Marta

last: Rodriguez

first: Ruth

last: Alonso-Alonso

last: Tomas-Roca

first: Socorro

last: Rodriguez-Pinilla

first: Rebeca

last: Manso

last: Cereceda

first: Jennifer

last: Borregon

first: Teresa

last: Villaescusa

first: Raul

last: Cordoba

first: Margarita

last: Sanchez-Beato

first: Ismael

last: Fernandez-Miranda

first: Isabel

last: Betancor

first: Carmen

last: Barcena

first: Juan

middle: F

last: Garcia

first: Manuela

last: Mollejo

first: Monica

last: Garcia-Cosio

first: Paloma

last: Martin-Acosta

first: Fina

last: Climent

first: Dolores

last: Caballero

first: Lorena

last: de la Fuente

first: Pablo

last: Minguez

first: Linda

last: Kessler

first: Catherine

last: Scholz

first: Antonio

last: Gualberto

first: Rufino

last: Mondejar

first: Miguel

last: Piris


title: Transcriptional profiling of whisker follicles and of the striatum in methamphetamine self-administered rats

status: Public on Aug 27 2021

city: Daegu

first: Taekwon

last: Son

address: 61, Cheomdan-ro, Dong-gu

department: Korea Brain Bank

country: South Korea

institute: Korea Brain Research Institute

type: Expression profiling by high throughput sequencing

summary: This study provides the first data on gene expression levels in whisker follicles and in the striatum in relation to MA reward and thereby may accelerate the research on the whisker follicle as an alternative source of biomarkers for the diagnosis of MA use disorder.

overall_design: Four groups - striatum or whisker follicle treated with saline or methamphetamine

first: Won-Jun

last: Jang

first: Sooyeun

last: Lee

first: Chul-Ho

last: Jeong


title: Genome-wide identification of RNA-chromatin interactions in Arabidopsis

city: Beiing

first: Yijun

last: Qi

address: NO.1 Qinghuayuan

department: School of Life Sciences

country: China

institute: Tsinghua University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: It is increasingly evident that various RNA molecules can bind chromatin to regulate gene expression and genome organization. Here we adapted a sequencing-based technique to profile RNA-chromatin interactions at a genome-wide scale in Arabidopsis seedlings. We identified more than ten thousand RNA-chromatin interactions mediated by protein-coding RNAs, long non-coding RNAs (ncRNAs) and small ncRNAs in Arabidopsis. These RNAs preferentially target genic regions, especially exonic regions. Protein-coding RNAs primarily engage in local and cis-chromosomal interactions, whereas long ncRNAs (lncRNAs) and small ncRNAs preferentially engage in trans-chromosomal interactions. RNA-chromatin interactions tend to positively correlate with DNA-DNA interactions, suggesting a role of DNA-DNA interactions in confining RNA-chromatin interactions and/or a role of RNA-chromatin interactions in shaping genome organization at a global level. We further show that some RNA-chromatin interactions undergo alterations in response to biotic and abiotic stresses. Our study provides a global view of RNA-chromatin interactions in Arabidopsis and a rich resource for future investigation of the regulatory roles of RNAs in gene expression and genome organization.

overall_design: To identify chromatin-associated RNAs and their target sites in Arabidopsis, we conducted GRID-seq using Arabidopsis wild-type Col-0 seedlings. To evaluate the contribution of RNA transcription level to the abundance of RNAs detected in GRID-seq, we conducted global nuclear run-on sequencing (Gro-seq) to detect the levels of nascent RNAs and compared RNA reads in GRID-seq and Gro-seq. To determine the overlap between RNA-chromatin interactions and DNA-DNA interactions, we conducted BL-Hi-C and compared interactions identified by GRID-seq and BL-Hi-C. To determine whether RNA-chromatin interactions are dynamic and respond to environmental cues, we conducted GRID-seq using heat-treated and DC3000-treated seedlings.

first: Lanxia

last: Li

first: Haofei

last: Luo

first: Lu

last: Han

first: Yan


title: Intergenerational inheritance of trained immunity and heterologous resistance to infections (RRBS - DNA methylation)

city: Saarbrücken

first: Kathrin

last: Kattler-Lackes

state: non-US Resident

address: Campus A2.4 Raum 0.13

department: Epigenetics

country: Germany

institute: Saarland University

type: Methylation profiling by high throughput sequencing

summary: Intergenerational inheritance (Inter-I) of phenotypic characteristics has been demonstrated in plants and invertebrates, with epigenetic modifications playing a role in the inheritance of a variety of features such as appearance1, adaptation to stress, or resistance to infections. Here we provide evidence of Inter-I of transcriptional and epigenetic signatures of trained immunity to the progeny of mice that survived a sublethal systemic Candida albicans infection. Intergenerational trained mice (F1) presented with significant cellular, developmental, transcriptional, and epigenetic changes within the bone marrow resident myeloid effector and progenitor cell compartment. These alterations led to an enhanced responsiveness to in vivo endotoxin challenge and Escherichia coli infection, providing the offspring with protection against heterologous infections. These results argue for the contribution of Lamarckian evolutionary processes to protect against infections in vertebrates.

overall_design: Male mice were infected with subletal dose of C. albicans. One month after clearance of the infection, ‘resting’ (mock-infected with PBS, F0R) and the ‘trained’ (C. albicans-infected and recovered, F0T) mice were mated with healthy non-infected females. DNA methylomes of 10 isogenic control males and 10 infected and recovered males using a comprehensive HaeIII restriction based RRBS (reduced representation bisulfite sequencing) approach.

last: Kattler

first: Gilles

last: Gasparoni

first: Kostya

last: Lepikhov

first: Joern

last: Walter


title: EpiPanGI Dx: A cell-free DNA methylation fingerprint for the early detection of gastrointestinal cancers

city: Houston

first: Jianfeng

last: Xu

state: Texas

address: one baylor plaza

country: USA

institute: Baylor College of Medicine

summary: Owing to high cancer-specificity, DNA methylation alterations have emerged as front-runners in cell-free DNA (cf-DNA) biomarker development. However, much effort to date has focused on single cancers and have not explored the possibility of developing a pan-cancer diagnostic assay. Here, we undertook a genome-wide DNA methylation analysis for multiple gastrointestinal (GI) cancers, to develop a panGI diagnostic assay. By analyzing the DNA methylation data from 1940 tumor and adjacent normal tissues from TCGA and GSE72872 datasets, we first identified the differentially methylated regions (DMRs) between individual GI cancers and adjacent normal tissues, as well as across all GI cancers. We next prioritized a list of 67,832 tissue DMRs encompassing a 25.6 Mb genomic region by incorporating all significant DMRs across various GI cancers to design a custom SeqCap Epi, targeted bisulfite sequencing platform. Subsequent investigation of these tissue-specific DMRs in 300 cf-DNA specimens and applying machine learning algorithms led to the development of three distinct categories of DMR panels: 1) Cancer-specific biomarker panels with an AUC values of 0.98 (Colorectal cancer, CRC), 0.94 (Esophageal squamous cell carcinoma, ESCC), 0.90 (Esophageal adenocarcinoma, EAC), 0.90 (Gastric cancer, GC), 0.98 (Hepatocellular carcinoma, HCC), and 0.85 (Pancreatic ductal adenocarcinoma, PDAC); 2) A pan-GI panel that detected all GI cancers with an AUC of 0.90; and 3) A multi-cancer prediction panel, EpiPanGI Dx, with a prediction accuracy around 0.85-0.95 for most GI cancers. Utilizing a novel biomarker discovery approach, we provide first evidence for a cell-free DNA methylation biomarker assay that offer a robust diagnostic accuracy for all gastrointestinal cancers.

overall_design: Targeted DNA methylation sequencing in cell-free DNA from 300 plasma samples collected across gastrointestinal cancers and healthy controls

first: Ajay

last: Goel

first: Raju

last: Kandimalla

first: Wei


title: Host and pathogen gene expression during early infection of soybean seedlings by Phytophthora sojae, analyzed by ABI Solid RNA sequencing

status: Public on Aug 28 2021

city: Corvallis

first: Brett

middle: Merrick

last: Tyler

state: OR

address: ALS3021, 2750 Campus Way

department: Center for Quantitative Life Sciences

institute: Oregon State University

summary: Hypocotyls of soybean (Glycine max) seedlings of cultivar Williams were inoculated with mycelia of the oomycete pathogen Phytophthora sojae grown in liquid V8 medium or the hypocotyls were mock inoculated. After 12 hours, the sites of inoculation were excised from the hypocotyls and frozen for RNA extraction. Phytophthora sojae mycelia used for inoculation was saved for RNA extraction also

sample_organism:
Glycine max
Phytophthora sojae

platform_organism:
Glycine max
Phytophthora sojae

overall_design: Four replicate experiments were conducted. Each replicate consisted of 30 P. sojae-inoculated or mock-inoculated hypocotyls, as well as a sample of the P. sojae mycelia used for the 30 inoculations

first: Lecong

last: Zhou

first: Matthew

last: Dyer


title: Toxicity after AAV delivery of RNAi expression constructs into nunhuman primate brain

city: Philadelphia

first: Paul

middle: T

last: Ranum

state: PA

address: 3501 Civic Center Blvd.

department: Center for Cellular and Molecular Therapy

institute: The Children's Hospital of Philadelphia

type: Non-coding RNA profiling by high throughput sequencing

summary: RNA Seq and small RNA Seq datasets from cerebellum of Rhesus macaque from treated and control cohorts.

overall_design: RNA Seq experiments performed in association with the Keiser et al 2021 publication in Nature Medicine fall into two categories "Study1" and "Study2". Study1 denotes experiments that were  performed in an effort to identify the cause of toxicity observed after administration of the rAAV2/1.miS1 (hereafter referred to as AAV.miS1) construct.  Study2 designates samples that were generated in experiments desgned to test new construct configurations including "AAV.intmiS1", "AAV.miSCA7", and "AAV.stuffer" which each represent a AAV capsid carrying different cargo configurations.  The purpose of Study2 was to assess and characterize the immune responses generated by each of these constructs.

first: Megan

middle: K

last: Keiser

first: Beverly

middle: L

last: Davidson


title: Co-evolving JAK2V617F+ relapsed AML and donor T cells with PD-1 blockade after stem cell transplantation: an index case [CITE-seq]

city: Boston

first: Livius

last: Penter

state: MA

address: 450 Brookline Avenue

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: JAK2V617+ myeloproliferative disease has been reported to overexpress PD-L1 rationalizing therapeutic PD-1 blockade. We performed an integrated single cell analysis on samples from an exceptional responder to nivolumab to elucidate determinants of response in this patient.

overall_design: Mononuclear cells from peripheral blood were obtained from one patient with transient response to nivolumab and sequenced using 5' scRNA-seq/CITE-seq/scTCR-seq/scBCR-seq on the 10x platform. Gene expression (scRNA-seq) and antibody capture (CITE-seq) are contained in the same feature matrix. scTCR-seq and scBCR-seq are provided individually. Raw reads of gene expression are provided as bam files and raw reads of CITE-seq, scTCR-seq and scBCR-seq as fastq files.

first: L

first: S

middle: H

last: Gohil

first: P

last: Bachireddy

first: Catherine

middle: J

last: Wu


title: Functional Human Genes Typically Exhibit Epigenetic Conservation

city: Los Angeles

first: Darryl

last: Shibata

state: CA

address: NOR 1441 Eastlake Ave

department: Pathology

institute: USC

type: Methylation profiling by genome tiling array

summary: Recent DepMap CRISPR-Cas9 single gene disruptions have identified genes more essential to proliferation in tissue culture. It would be valuable to translate these finding with measurements more practical for human tissues. Here we show that DepMap essential genes and other literature curated functional genes exhibit cell-specific preferential epigenetic conservation when DNA methylation measurements are compared between replicate cell lines and between intestinal crypts from the same individual. Culture experiments indicate that epigenetic drift accumulates through time with smaller differences in more functional genes. In NCI-60 cell lines, greater targeted gene conservation correlated with greater drug sensitivity. These studies indicate that two measurements separated in time allow normal or neoplastic cells to signal through conservation which human genes are more essential to their survival in vitro or in vivo.

overall_design: Methylation was measured from DNA extracted from single human crypts or glands using the Restore Illumina Protocol

first: Daniel

middle: M

last: Rud


title: Co-evolving JAK2V617F+ relapsed AML and donor T cells with PD-1 blockade after stem cell transplantation: an index case [TCR-seq]


title: RNA-Seq of liver from CLA-exposed mice with/without PPARα antagonist

city: Yangzhou

first: Demin

last: Cai

address: Daxue South Road 88

institute: Yangzhou University

summary: We demonstrate that conjugated linoleic acid (CLA), when given to mice as a dietary supplement, induced an enlarged liver and hepatic steatosis. The progression of NAFLD and insulin resistance was reversed by GW6471 a small-molecule antagonist of PPARα. Transcriptional profiling of livers unraveled that genes involved in lipid metabolism core gene programs controlled by PPARα in response to CLA and GW6471.Our findings reveal a novel role of PPARα in the regulation of lipid homeostasis and highlight its druggable nature in NAFLD.

overall_design: Hepatic mRNA profiles of  mice treated with CLA or  PPARα antagonist or CLA combined PPARα antagonist

first: Hao-yu

last: Liu

first: Bo


title: RNA-sequencing data and whole transcriptome analysis from CDH2 knock-in mice, modeling attention-deficit hyperactivity disorder (ADHD)

city: Be'er Sheva

last: Halperin

address: Ben Gurion 1 st

country: Israel

institute: Ben-Gurion University of the Negev

summary: Here we demonstrate familial ADHD caused by a missense mutation in CDH2, which encodes the adhesion protein N-cadherin, known to play a significant role in synaptogenesis; In line with the human phenotype, CRISPR/Cas9-mutated knock-in mice harboring the human p.H150Y mutation in the mouse ortholog recapitulated core behavioral features of hyperactivity. Symptoms were modified by methylphenidate, the most commonly prescribed therapeutic for ADHD. The mutated mice exhibited impaired presynaptic vesicle clustering, attenuated evoked transmitter release and decreased spontaneous release. Specific downstream molecular pathways were affected in both the ventral midbrain and prefrontal cortex, with reduced tyrosine hydroxylase expression and dopamine levels. We thus delineate roles for CDH2-related pathways in the pathophysiology of ADHD.

overall_design: Prefrontal cortex and ventral mid-brain neuronal mRNA profiles of 16 male 13-week-old wildtype (WT) and CRISPR/Cas9-mutated knock-in mice (harboring the specific human p.H150Y substitution)

first: Ohad

middle: S

last: Birk


title: Co-evolving JAK2V617F+ relapsed AML and donor T cells with PD-1 blockade after stem cell transplantation: an index case [RNA-seq]


title: Co-evolving JAK2V617F+ relapsed AML and donor T cells with PD-1 blockade after stem cell transplantation: an index case [BCR-seq]


title: Co-evolving JAK2V617F+ relapsed AML and donor T cells with PD-1 blockade after stem cell transplantation: an index case [ATAC-seq]

overall_design: Mononuclear cells from peripheral blood were obtained from one patient with transient response to nivolumab and sequenced using mtscATAC-seq on the 10x platform


title: Pharmacological inhibition of CDK4/6 augments long-term anti-tumor immunity through the induction of T cell memory [13_RNAseq_in_vitro_mouse]

status: Public on Aug 25 2021

city: Melbourne

first: Emily

middle: Jane

last: Lelliott

state: VIC

address: 305 Grattan Street

department: Research

country: Australia

institute: Peter MacCallum Cancer Centre

summary: Small molecule inhibitors of cyclin dependent kinases 4 and 6 (CDK4/6) are an approved treatment for hormone receptor-positive breast cancer and are currently under evaluation across hundreds of clinical trials for other cancer types. The clinical success of these inhibitors is largely attributed to well-defined tumor-intrinsic cytostatic mechanisms, while their emerging role as immunomodulatory agents is less understood. Using integrated epigenomic, transcriptomic and proteomic analyses, we demonstrated a novel action of CDK4/6 inhibitors in promoting the phenotypic and functional acquisition of immunological T cell memory. Short-term priming with a CDK4/6 inhibitor promoted long-term endogenous anti-tumor T cell immunity in mice,  enhanced the persistence and therapeutic efficacy of chimeric antigen receptor (CAR)-T cells, and induced an RB-dependent T cell phenotype supportive of favorable responses to immune checkpoint blockade in melanoma patients. Taken together, these mechanistic insights significantly broaden the prospective utility of CDK4/6 inhibitors as clinical tools to boost anti-tumor T cell immunity.

overall_design: RNA sequencing of OT-I CD8+ T cells peptide-activated in vitro for 72h, washed and cultured for a further 24h + DMSO/palbociclib in triplicate

first: Stephin

last: Vervoort

first: Conor

last: Kearney

first: Karen

middle: E

last: Sheppard


title: RNAseq of the retinas of diabetic Goto-Kakizaki (GK) rats treated with spironolactone

city: Paris

first: Min

last: ZHAO

state: France

address: 15 rue de l'Ecole de Médecine

country: France

institute: INSERM U1138, Centre de Recherche des Cordelier, University Paris Descartes

summary: To identify the transcriptional regulatory mechanisms associated with the biological anti-edematous and anti-inflammatory effect of spironolactone, we performed an analysis of the regulated genes in the neuroretina of GK rats aged 14 months and treated with a formulation of Spironolacton-loaded Microspheres (Sp-MSs) that released spironolactone for at least 2 months (mean size 30µm, 1µg/mg MSs/day). RNA-sequencing was performed on the neural retina and non-loade microspheres (NL-MSs) served as control treatment. The heatmaps of genes differentially regulated by Sp-MSs individuals as compared to NL-MSs showed a clear difference between the two conditions with 114 genes significantly regulated between the two groups, 27 significantly down regulated and 87 significantly up regulated  (Log2FC ≥ 0,5, adjusted p<0.05). Pathway enrichment analysis using hallmark gene-set function highlighted 9 significantly regulated pathways: unfolded protein response, UV response, G2M checkpoint, allograft rejection, interferon gamma response, MTORC1 signaling, oxidative phosphorylation, MYC targets and adipogenesis (Figure EV 3B, C). Genes encoding proteins known to intervene in vascular permeability and retinal edema were counter regulated by Sp-MSs including Vldlr, Sesn2, Adcyap1, Dusp8, Pten, Slc7a1, Tjp1, Dlg1, Sema7a, although Vegf was rather up-regulated, suggested an anti-edematous mechanism independent from VEGF. The effect of Sp-MSs was confirmed by quantitative PCR for number of these genes demonstrating that spironolactone acts as a transcriptional regulator to normalize the diabetic retina.

overall_design: Retinal mRNA profiles of 14-month GK rats treated with intravitreal Sp-Mss vs. NL-MSs

last: Zhao

first: Justine

last: Guegan

first: Francine

last: Behar-Cohen


title: Co-evolving JAK2V617F+ relapsed AML and donor T cells with PD-1 blockade after stem cell transplantation: an index case

first: Livius

last: Penter

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Antihypertensive drug treatment and susceptibility to SARS-CoV-2 infection in human PSC-derived cardiomyocytes and primary endothelial cells

city: Tucson

first: Jared

last: Churko

state: Arizona

address: 1501 N CAMPBELL AVE LSN 461

department: CMM

institute: University of Arizona

summary: hPSC-derived cadiomyocytes and primary endothelial cells were treated with lisinopril or losartan to assess whether antihypertensive drugs could impact SARS-CoV-2 entry in vitro

overall_design: The pathogenicity of SARS-CoV-2 has been attributed to its ability to enter through the membrane bound angiotensin-converting enzyme 2 (ACE2) receptor. Therefore, it has been heavily suspected that angiotensin converting enzyme inhibitor (ACEI) or angiotensin receptor blocker (ARB) therapy may affect the susceptibility of patients to SARS-CoV-2 infection. In this study, we used human pluripotent stem cell-derived cardiomyocytes (hPSC-CMs) and primary human endothelial cells (hECs) to assess whether SARS-CoV-2 infection levels change in the presence of two widely prescribed antihypertensive medications, losartan and lisinopril, and to identify differences in the transcriptomic signatures of hPSC-CMs exposed to SARS-CoV-2. Significant enrichment of protein coding genes involved in inflammation, immunity and cardiomyocyte structural proteins were identified in SARS-CoV-2 treated cells. However, in vitro treatment of lisinopril or losartan in hPSC-CMs or hECs did not affect the susceptibility of cells to SARS-CoV-2 infection.


title: Cish attenuates homeostatic cytokine signaling to promote lung-specific macrophage programming and function

city: Pittsburgh

first: Rachel

middle: A.

last: Gottschalk

state: Pennsylvania

address: 200 Lothrop St., W1047 BST

department: Immunology

institute: University of Pittsburgh

summary: Lung-specific expression of the SOCS family member Cish is driven by steady-state GM-CSF signaling and shapes alveolar macrophage identity and homeostatic function.

overall_design: Gene expression in alveolar macrophages from WT and Cish-/- mice

middle: A

first: Karsen

last: Shoger

first: Neha

last: Cheemalavagu


title: Pharmacological inhibition of CDK4/6 augments long-term anti-tumor immunity through the induction of T cell memory [11_RNAseq_in_vitro_mouse_HER2_CAR]

overall_design: RNA sequencing of mouse HER2 CAR T cells CD3/28-activated in vitro for 72h and treated for 24h with DMSO/palbociclib in triplicate


title: Relevance of microRNAs to the regulation of the brain-placental axis in mice

city: Columbia

first: Susanta

middle: K.

last: Behura

state: Missouri

address: 920 East Campus Drive

department: Division of Animal Sciences

institute: Univeristy of Missouri

summary: We performed deep sequencing of small RNA in the fetal brain and placenta of male and female fetuses to study expression pattern of miRNA and identify key miRNAs that are relevant to gene regulation of the brain-placental axis

overall_design: The day 15 mice placenta and brain samples of male and female fetuses were analyzed by miRNA-seq.

first: Monica

last: Strawn

first: Ananya

last: Samal

first: Md Bodruzzaman

last: Sarker

first: Pramod

last: Dhakal


title: Pharmacological inhibition of CDK4/6 augments long-term anti-tumor immunity through the induction of T cell memory [10_RNAseq_in_vitro_Jurkat]

first: Emily

last: Lelliott

overall_design: WT or RB1-/- Jurkat cells were treated for 72h with DMSO/palbociclib in triplicate

last: Vervoort


title: Pharmacological inhibition of CDK4/6 augments long-term anti-tumor immunity through the induction of T cell memory

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Pharmacological inhibition of CDK4/6 augments long-term anti-tumor immunity through the induction of T cell memory [12_RNAseq_in_vitro_mouse_rb_and_thy]

overall_design: RNA sequencing of WT or Rb1-knockout mouse CD8+ T cells CD3/28-activated in vitro for 48h and treated for 48h with DMSO/palbociclib/thymidine in triplicate

first: Stephin

last: Kearney

last: Sheppard


title: Pharmacological inhibition of CDK4/6 augments long-term anti-tumor immunity through the induction of T cell memory [9_RNAseq_in_vitro_human_LeY_CAR]

overall_design: RNA sequencing of human Lewis Y CAR T cells CD3-activated in vitro for 8 days and treated for 7 days with DMSO/palbociclib in duplicate

first: Conor


title: Pharmacological inhibition of CDK4/6 augments long-term anti-tumor immunity through the induction of T cell memory [04_in_vitro]

overall_design: OT-I CD8+ T cells were peptide-activated in vitro for 72h, washed and cultured for a further 24h + DMSO/palbociclib. Treated cells were then labelled with oligo-barcoded hashtagging antibodies (HTO) and captured for single-cell sequencing of RNA (GEX) and HTO. A total of two samples (DMSO and Palbo) were hashtagged and pooled for a single capture reaction.

first: Karen


title: Pharmacological inhibition of CDK4/6 augments long-term anti-tumor immunity through the induction of T cell memory [8_RNAseq_ex_vivo_mouse]

overall_design: RNA sequencing of CD8+ T cells from MC38-OVA tumors treated for 7 days with vehicle or palbociclib (3 replicates per group, each representative of 4 tumors pooled)


title: Regulation of intestinal immunity and tissue repair by enteric glia  (Bulk gene expression analysis of  small intestinal glia cells in naïve and H. poly-infected mice.)

city: London

first: Vassilis

last: Pachnis

state: London

address: 1 Midland Road

department: Development and Homeostasis of the Nervous System Laboratory

country: United Kingdom

institute: The Francis Crick Institute

summary: Tissue maintenance and repair depend on the integrated activity of multiple cell types. Whereas the contributions of epithelial, immune and stromal cells in intestinal tissue integrity are well understood, the role of intrinsic neuroglia networks remains largely unknown. Here, we uncover pivotal roles of enteric glial cells (EGCs) in intestinal homeostasis, immunity and tissue repair. We demonstrate that infection of mice with Heligmosomoides polygyrus (H. poly) leads to enteric gliosis and upregulation of the interferon gamma (IFN-γ) gene signature. Single-cell transcriptomics of tunica muscularis (TM) showed that glia-specific abrogation of IFN-γ signaling leads to tissue-wide activation of pro-inflammatory transcriptional programs. In addition, disruption of the IFN-γ-EGC signaling axis enhanced the inflammatory and granulomatous response of TM to helminths. Mechanistically, we show that upregulation of Cxcl10 is an early immediate response of EGCs to IFN-γ signaling and provide evidence that this chemokine and the downstream amplification of IFN-γ signaling in the TM are required for a measured inflammatory response to helminths and resolution of granulomatous pathology. Our study demonstrates that IFN-γ signaling in enteric glia is central to intestinal homeostasis and reveals critical roles of the IFN-γ-EGC-Cxcl10 axis in immune response and tissue repair following infectious challenge.  To characterize the response of enteric glia to helminth infection, we performed bulk RNAseq  of tdT+ cells (=EGCs) and tdT- cells (=non-glia cells) from the TM of naïve and H. poly-infected Sox10CreERT2;Rosa26tdTomato mice.

overall_design: To investigate how EGCs respond to pathogen invasion, tamoxifen-treated Sox10CreERT2;Rosa26tdTomato mice, which express the fluorescent reporter tdTomato (tdT) specifically in the intrinsic glia cell network of the gut, were infected with H. poly. At 7 days post, we isolated enteric glia cells (EGCs, tdT+) and non-glia cells (tdT-) using FACS from four individual mice for each treatment condition (4x EGC Control = EnGliaCtrl, 4x non-glia Control = EnNonGliaCtrl, 4x EGC H.poly = EnGliaInf, 4x non-glia H.poly = EnNonGliaInf)

first: Franze

last: Progatzky

first: Stefan

last: Boeing


title: Pharmacological inhibition of CDK4/6 augments long-term anti-tumor immunity through the induction of T cell memory [02_patient_samples]

overall_design: PBMC were isolated from a melanoma patient during the course of their treatment with combination palbociclib and binimetinib (palbo/bini) for one month, followed by a switch to ipilimumab and nivolumab (ipi/nivo). Samples were collected and cryopreserved prior to and 2 weeks into treatment with palbo/bini, and prior to and 1 month into treatment with ipi/nivo. Following collection of all PBMC samples, T cells were isolated and labelled with oligo-tagged antibodies specific for CD4, CD8, PD-1, TIM3, IL7R, CD7, CXCR3 and CD39 (antibody-derived tags; ADT) and oligo-barcoded hashtagging antibodies (HTO). Labelled cells were then captured for single-cell sequencing of RNA (GEX), TCR (VDJ), ADT and HTO. A total of 4 samples were hashtagged and pooled for a single capture reaction.


title: Pharmacological inhibition of CDK4/6 augments long-term anti-tumor immunity through the induction of T cell memory [7_ChIPseq_in_vitro_mouse]

overall_design: ChIP sequencing of OT-I CD8+ T cells peptide-activated in vitro for 72h, washed and cultured for a further 6h + DMSO/palbociclib in duplicate


title: Pharmacological inhibition of CDK4/6 augments long-term anti-tumor immunity through the induction of T cell memory [5_ATACseq_ex_vivo_mouse]

overall_design: ATAC sequencing of CD8+ T cells from MC38-OVA tumors treated for 7 days with vehicle or palbociclib (2 replicates per group, each representative of 4 tumors pooled)


title: Singel cell RNA-seq  analysis of ARPKD mutation affect hepatic organoid differentiation

city: Stanford

first: Zhuoqing

last: Fang

state: California

address: 300 Pasteur Drive

institute: Stanford

summary: Liver fibrosis usually involve different cell types interaction. Despite its devastating consequences, there are no treatments for liver fibrosis. Genome engineering and a human hepatic organoid system was used to produce the first naïve in vitro model including several crucial components contributed for liver fibrosis. Hepatic organoids engineered to express the most common causative mutation for Autosomal Recessive Polycystic Kidney Disease (ARPKD) developed abnormal bile ducts and hepatic fibrosis in only 21 days, which are the key features of ARPKD liver pathology. Singel cell level analysis indicated that the ARPKD mutation induced bile duct proliferation through several critial pathways, and appear to be actively involved in collagen fiber generation. Therefore, abnormal cholangiocytes promotes the expansion its counterpart , which collagen-producing myofibroblasts with a markedly increased level of PDGFRB protein expression and evidence of an activated STAT3 signalling pathway.

overall_design: To study transcriptomic changes during iPSC-HB-HOs differentiation between control and ARPKD, Firstly, we compared 3 control vs 3 ARPKD donors at HO stage; then we compared those paires at all iPSC-HB-HO stages using 10x Chromium based single cells RNA-seq platform. We used 'demuxlet' and cell hashing pipeline to multiplex sample input for single cell RNA-seq, which rely on decode genetic variation and cell labeling respectively.

first: YUAN

last: GUAN

first: Meiyue

last: Wang


title: Pharmacological inhibition of CDK4/6 augments long-term anti-tumor immunity through the induction of T cell memory [03_in_vivo]

overall_design: OT-I CD8+ T cells were peptide-activated in vitro for 72h, washed and cultured for a further 24h + DMSO/palbociclib. Treated cells were transferred into C57BL/6 and then reisolated from spleen after 30 days. Isolated cells were labelled with oligo-barcoded hashtagging antibodies (HTO) and captured for single-cell sequencing of RNA (GEX) and HTO. A total of two samples (DMSO and Palbo) were hashtagged and pooled for a single capture reaction.


title: Identification of LncRNAs Differentially Expressed in the Serum of Alzheimer’s patients

city: Harbin

first: qichang

last: gao

state: Heilongjiang

address: youzheng street, Nangang district

department: orthopedics departmnet

institute: First Affiliated Hospital of Harbin Medical University

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: Alzheimer’s disease (AD) is a common primary senile neurodegenerative disease which is the most common cause of dementia. The clinical manifestations are mainly progressive memory decline, cognitive dysfunction, behavioral abnormalities and personality disorders. Due to the unclear pathogenesis and the complexity of the pathogenesis, no AD drugs can reverse the disease process. Therefore, it is particularly important to reveal the underlying mechanism of AD. Many studies  indicate that it is a multifactorial disease. However, the role of LncRNAs in the pathogenesis of AD remains unclear. In order to identify the transcriptional regulators of AD, we compared the expression of LncRNA in serum of AD patients and healthy volunteers by microarray analysis. This analysis revealed a set of LncRNAs specifically regulated in AD patients. These findings imply that lncRNA may play an important role in AD.

overall_design: The LncRNAs expression profiles in serum of 3 Alzheimer’s patients and 3 normal were analyzed by microarray analysis.

first: Fulin

last: Guan

first: Jiaao

last: Gu


title: IL12 integrated into the CAR exodomain converts CD8+ T cells to poly-functional NK-like cells with superior killing of antigen-loss tumors

status: Public on Aug 24 2021

city: Cologne

first: Agapios

last: Sachinidis

state: NRW

address: Robert-Kochstr. 39

department: Institute of Neurophysiology

institute: University of Cologne

summary: Chimeric antigen receptor (CAR)-redirected T cell therapy often fails to control tumors in the long-term due to selecting cancer cells that down-regulated or lost CAR targeted antigen. To reprogram the functional capacities of CAR T cells, we inserted IL12 into the extracellular moiety of a CD28- CAR; both the CAR and IL12 were functional indicated by antigen-redirected activation and STAT4 phosphorylation, respectively. CD8+ T cells engineered with a IL12-CAR gained a so far not recognized NK cell-like RNA expression signature and a CD94+CD56+CD62Lhigh phenotype closely similar, but not identical, to NK and cytokine activated killer (CIK) cells. IL12-CAR T cells with specificity for CEA additionally acquired antigen-independent, HLA-E restricted cytotoxicity eliminating both CEA-negative and CEA-positive cancer cells in an antigen-dependent and independent fashion that was in contrast to conventional CEA CAR T cells. Simultaneous signaling through CD3 of the CAR and through IL12 were required and sufficient for inducing NK-like cytotoxicity. Overall, we present a prototype of a new family of CARs that harbor a cytokine integrated into the extracellular module in order to reprogram the functional capacities of CAR T cells towards augmented tumor recognition and elimination.

overall_design: 6 samples were analysed, 3 triplicates (control: T cells engineered with conventional CAR, sample 1, 2 and 3) and 3 samples T cells engineered with IL12-CAR, sample 4, 5 and 6)


title: Characterization of R-loop-interacting proteins in embryonic stem cells reveals roles in ribosomal RNA processing and gene expression

city: Worcester

first: Thomas

middle: G

last: Fazzio

state: Massachusetts

address: 364 Plantation Street, Lazare Research Building -560E

department: Molecular, Cell and Cancer Biology

institute: University of Massachusetts medical school

summary: We performed mRNA-seq on mouse embryonic stem cells, with four DEAD-box family proteins, DDX10, DDX24, DDX27, DDX54 being partially depleted using RNA interference. Knockdown of EGFP was carried out as a control. By comparing all four knockdowns, we observed misregulation of a highly-overlapping set of genes, indicating that they regulate mRNA levels through a shared pathway.

overall_design: mRNA profiles of knockdowns of 4 Ddx genes, with EGFP knockdown as control, all performed with three biological replicates

first: Tong

last: Wu


title: Pharmacological inhibition of CDK4/6 augments long-term anti-tumor immunity through the induction of T cell memory [01_mouse_TIL]

overall_design: T cells were isolated from MC38-OVA tumors of mice that had been treated for one week with vehicle or palbociclib. Isolated T cells were labelled with oligo-tagged antibodies specific for PD1, Tim3, CD4 and CD8 (antibody-derived tags; ADT) and oligo-barcoded hashtagging antibodies (HTO). Labelled cells were then captured for single-cell sequencing of RNA (GEX), ADT and HTO. Two samples per treatment group (a total of four samples) were hashtagged and pooled for a single capture reaction. Each hashtagged sample is representative of 8 tumors pooled.


title: Single-cell analysis reveals divergent responses of human dendritic cells to the MVA vaccine

first: Nicolas

last: Manel

address: 12 rue Lhomond

department: INSERM U932

institute: Institut Curie

summary: Modified vaccinia Ankara (MVA) is a live, attenuated human smallpox vaccine and a vector for the development of new vaccines against infectious diseases and cancer. Efficient activation of the immune system by MVA partially relies on its encounter with dendritic cells (DCs). MVA infection of DCs leads to multiple outcomes, including cytokine production, activation of costimulatory molecules for T cell stimulation, and cell death. Here, we examined how these diverse responses are orchestrated in human DCs. Single-cell analyses revealed that the response to MVA infection in DCs was limited to early viral gene expression. In response to the early events in the viral cycle, we found that DCs grouped into three distinct clusters. A cluster of infected cells sensed the MVA genome by the intracellular innate immunity pathway mediated by cGAS, STING, TBK1, and IRF3 and subsequently produced inflammatory cytokines. In response to these cytokines, a cluster of noninfected bystander cells increased costimulatory molecule expression. A separate cluster of infected cells underwent caspase-dependent apoptosis. Induction of apoptosis persisted after inhibition of innate immunity pathway mediators independently of previously described IRF-dependent or replication-dependent pathways and was a response to early MVA gene expression. Together, our study identified multiple mechanisms that underlie the interactions of MVA with human DCs.

overall_design: The scRNA-seq was done for monocyte-derived dendritic cells derived from two independent donors. Cells were FACS sorted for live cells. For each donor an infected sample 24 hpi and a corresponding uninfected sample were analysed.

first: Marius

last: Döring

first: Kevin

last: de Azevedo

first: Francesca

last: Nadalin


title: Dynamic transcriptional reprogramming leads to novel immunotherapeutic vulnerabilities in myeloma

first: Birgit

last: Knoechel

address: 450 Brookline Ave

department: pediatric oncology

institute: Dana Farber Cancer Institute

summary: While there is extensive evidence for genetic variation as a basis for treatment resistance, other sources of variation result from cellular plasticity. Using multiple myeloma as an example of an incurable lymphoid malignancy, we show how cancer cells modulate lineage restriction, adapt their enhancer usage and employ cell-intrinsic diversity for survival and treatment escape. By using single cell transcriptome and chromatin accessibility profiling, we show that distinct transcriptional states co-exist in individual cancer cells and that differential transcriptional regulon usage and enhancer rewiring underlie these alternate transcriptional states. We demonstrate that exposure to standard treatment further promotes transcriptional reprogramming and differential enhancer recruitment, while simultaneously reducing developmental potential. Importantly, treatment generates a novel complement of actionable immunotherapy targets, such as CXCR4, which can be exploited to overcome treatment resistance. Our studies therefore delineate how to transform the cellular plasticity that underlies drug resistance into novel immuno-oncologic therapeutic opportunities.

overall_design:
Single cell expression profiles of 9 patients with relapsed/refractory multiple myeloma and two normal donors.
Note: to protect Patient's privacy we didn't upload raw data for scATAC and Smartseq_htseq Samples.

first: Julia

last: Frede

first: Praveen

last: Anand

first: Noori

last: Sotudeh

first: Ricardo

middle: P

last: Rengifo

first: Monica

last: Nair

first: Hannah

last: Stuart

first: Andrew

last: Yee

first: Tushara

last: Vijaykumar

first: Johannes

last: Waldschmidt

first: Sayalee

last: Potdar

first: Jake

last: Kloeber

first: Antonis

last: Kokkalis

first: Valeriya

last: Dimitrova

first: Mason

last: Mann

first: Jacob

last: Laubach

first: Paul

last: Richardson

first: Kenneth

last: Anderson

first: Noopur

last: Raje

first: Jens

last: Lohr


title: KIAA0753 human fibroblasts treated with control media, Smoothened Agonist (SAG) or WNT3A

city: Columbus

first: Rolf

last: Stottmann

state: OHIO

address: 575 Children's Crossroads

department: Pediatrics

institute: Nationwide Children's Hospital

summary: Human fibroblasts from a control or a patient with compound heterozygous variants in KIAA0753 treated with SAG or WNT3A to test responses within canonical Hedgehog or WNT signaling.

overall_design: Cells were maintained in culture, serum starved, and treated with control media, SAG media or WNT3A media. Total RNA was purified from each treatment and used for RNA-Seq. All treatments and sequencing were done in triplicate.

first: Katherine

last: Inskeep

middle: W

first: Kathryn

middle: N

last: Weaver


title: Structured elements drive extensive circular RNA translation

city: St. Louis

first: Chun-Kan

last: Chen

state: MO

address: 660 S Euclid Ave

department: Cell Biology and Physiology

institute: Washington University in St. Louis

summary: The human genome encodes tens of thousands circular RNAs (circRNAs) with mostly unknown functions. Circular RNAs requires internal ribosome entry sites (IRES) if they are to undergo translation without 5’ cap. Here, we develop a high-throughput screen to systematically discover RNA sequences that can direct circRNA translation in human cells. We identify over 17,000 endogenous and synthetic sequences as candidate circRNA IRES. 18S rRNA complementarity and a structured RNA element positioned on the IRES are important for driving circRNA translation. Ribosome profiling and peptidomic analyses show extensive IRES-ribosome association, hundreds of circRNA-encoded proteins with tissue -specific distribution, and antigen presentation. We find that circFGFR1p, a protein encoded by circFGFR1 that is down regulated in cancer, functions as a negative regulator of FGFR1 oncoprotein to suppress cell growth during stress.  Systematic identification of circRNA IRES elements may provide important links among circRNA regulation, biological function, and disease.

overall_design: High-throughput oligo-split-eGFP-circRNA reporter screening assay for obtaining cap-independent translation measurements of 55,000 fully designed sequences in parallel on circRNA using fluorescence-activated cell sorting and high-throughput DNA sequencing (FACS-seq).

first: Ran

last: Cheng

first: Janos

last: Demeter

first: Jin

first: Shira

last: Weingarten-Gabbay

first: Lihua

last: Jiang

first: Michael

last: Snyder

first: Jonathan

last: Weissman

first: Eran

last: Segal

first: Peter

last: Jackson

first: Howard

middle: Y

last: Chang


title: Induced muscle progenitor cells [ATAC-seq]

first: Fei

last: Ji

address: 185 Cambridge St

institute: Massachusetts General Hospital

summary: The generation of myotubes from fibroblasts upon forced MyoD expression is a classic example of factor-induced reprogramming in mammals. We recently discovered that additional modulation of signaling pathways with small molecules facilitates reprogramming to more primitive induced muscle progenitor cells (iMPCs). However, the mechanisms by which a single transcription factor drives differentiated cells into distinct developmental states remain unknown. We therefore dissected the transcriptional and epigenetic dynamics of fibroblasts undergoing MyoD-dependent reprogramming to either myotubes or iMPCs using a novel MyoD transgenic model. To this end, we performed ATAC sequencing for Pax7-nGFP positive iMPCs/satellite cells, cells undergoing dedifferentiation (i.e. Dox+FRG) or transdifferentiation (i.e. Dox) and cells overexpressing a wild type MyoD or a mutant MyoD (i.e. MN) in the presence of FRG. Our analyses elucidate the role of MyoD in myogenic reprogramming and derive general principles by which transcription factors and signaling pathways cooperate to rewire cell identity. Our results may also inform on potential therapeutic applications of direct reprogramming.

overall_design: ATAC-seq was performed for 14 samples in duplicate.

first: Masaki

last: Yagi

first: Ruslan

middle: I

last: Sadreyev

first: Konrad

last: Hochedlinger


title: Induced muscle progenitor cells [RNA-seq]

summary: The generation of myotubes from fibroblasts upon forced MyoD expression is a classic example of factor-induced reprogramming in mammals. We recently discovered that additional modulation of signaling pathways with small molecules facilitates reprogramming to more primitive induced muscle progenitor cells (iMPCs). However, the mechanisms by which a single transcription factor drives differentiated cells into distinct developmental states remain unknown. We therefore dissected the transcriptional and epigenetic dynamics of fibroblasts undergoing MyoD-dependent reprogramming to either myotubes or iMPCs using a novel MyoD transgenic model. To this end, we performed RNA-sequencing for Pax7-nGFP positive (including high and low) iMPCs/satellite cells, cells undergoing dedifferentiation (i.e. Dox+FRG) or transdifferentiation (i.e. Dox) and cells overexpressing a wild type MyoD or a mutant MyoD (i.e. MN) in the presence of FRG. Our analyses elucidate the role of MyoD in myogenic reprogramming and derive general principles by which transcription factors and signaling pathways cooperate to rewire cell identity. Our results may also inform on potential therapeutic applications of direct reprogramming.

overall_design: RNA-seq was performed for 14 samples in duplicate.


title: BMP receptor blockade overcomes extrinsic inhibition of remyelination and restores neurovascular homeostasis

city: San Francisco, CA

first: Katerina

last: akassoglou

address: 1650 Owens st

institute: Gladstone Institutes

summary: Extrinsic inhibitors at sites of blood-brain barrier (BBB) disruption and neurovascular damage contribute to remyelination failure in neurological diseases. However, therapies to overcome extrinsic inhibition of remyelination are not widely available and the dynamics of glial progenitor niche remodeling at site of neurovascular dysfunction are largely unknown. By integrating in vivo two-photon (2P) imaging co-registered with electron microscopy and transcriptomics in chronic neuroinflammatory lesions, we found repressed anticoagulation pathways in oligodendrocyte precursor cells (OPCs) that clustered perivascularly at sites of limited remyelination with deposition of fibrinogen, a blood coagulation factor abundantly deposited in multiple sclerosis lesions. By developing the OPC-X-screen to identify compounds that promote remyelination in the presence of extrinsic inhibitors, we showed that known promyelinating drugs did not rescue extrinsic inhibition of remyelination by fibrinogen. In contrast, bone morphogenetic protein (BMP) receptor blockade rescued the inhibitory fibrinogen effects and restored a promyelinating progenitor niche by promoting myelinating oligodendrocytes, while suppressing astrocyte cell fate with potent therapeutic effects in chronic models of multiple sclerosis. Thus, abortive OPC differentiation by fibrinogen is refractory to known promyelinating compounds, suggesting that blockade of the BMP signaling pathway may enhance remyelinating efficacy by overcoming extrinsic inhibition in neuroinflammatory lesions with vascular damage.

overall_design: See Methods sections of manucsript for details of sample processing and RNA-seq analysis. In brief, NG2-Tdtomato+ cells were FACS sorted from spinal cords of NG2-CreERTM:Rosa-tdTomato/+:Cx3cr1GFP/+ mice with or without EAE and processed for bulk RNA-seq analysis.

first: Andrew

last: Mendiola

first: Mark

last: Petersen

last: Akassoglou


title: RNA-seq of PCNA WT/PyMT mammary tumor cell and PCNA 211F mammary tumor cell

city: Taichung

first: Shao-Chun

last: Wang

address: No. 6 Xueshi Rd

country: Taiwan

institute: China Medical University Hospital

summary: To further understand the cellular function of PCNA Y211 phosphrylation, we have profiled RNA expression from our transgenic mouse model derived mammary tumor cell.

overall_design: 2 independent biological repeats of  PCNA WT/PyMT mammary tumor cell and PCNA 211F/PyMT mammary tumor cell

first: Yuan-Liang


title: Transcriptome changes in Drosophila HB10 cells in response to a temperature shift from 24 to 14°C

status: Public on Sep 13 2021

city: Zurich

first: Christian

middle: F.

last: Lehner

address: Winterthurerstrasse 190

department: DMLS

country: Switzerland

institute: University of Zurich

summary: Cells in ectothermic organisms often maintain homeostatic function over a considerable range of ambient temperatures.  However, as temperature has pronounced effects on all biological processes, but not necessarily in a uniform manner on each of the myriad of distinct processes, cellular acclimation to distinct temperatures is predicted to involve complex regulation. Initially, to assess the effects of temperature change within the readily tolerated temperature range on the transcriptome, we have performed expression profiling with S2R+ cells, a hemocyte-like cell line derived from the ectothermic organism Drosophila melanogaster. To adress the cell-type specificity of the transcriptome change induced by a temperature downshift from the optimal temperature to a temperature at the lower end of the readily tolerated range, we have performed an anologous experiment with cultured Drosophila HB10 cells. These cells with similarities to adult muscle cell progenitors have recently been derived from Drosophila embryos with the method (Simcox et al. 2008. PLoS Genetics 4, e1000142) involving expression of activated ras using Act5C-GAL4 in combination with UASt-ras85D[V12].

overall_design: Aliquots of HB10 cells were plated and shifted to different temperatures (24 and 14°C).  Twenty-four hours after the temperature shift, total RNA was isolated and processed for hybridization of microarrays. Three replicate experiments were preformed.

first: Stefano

last: Leo

middle: F


title: Analysis of cabazitaxel-resistant mechanism in human castration-resistant prostate cancer

city: Tokyo

first: Hiroshi

last: Hongo

state: Tokyo

address: 35, Shinanomachi, Shinjuku-ku

department: Urology

country: Japan

institute: Keio University School of Medicine

summary: To investigate cabazitaxel (CBZ) resistance in prostate cancer, we examined the changes in global gene expression before and after development of acquired CBZ resistance. Functional annotation clustering (FAC) analysis of DAVID showed cell division (GO: 0051301) and mitotic nuclear division (GO: 0007067) were the most enhanced clusters in PC3CR compared with PC3.

overall_design: PC3 and PC3CR cells were used for microarrays. PC3CR cells were newly established in our laboratory, which were grown and passaged upon reaching confluence in medium containing CBZ over a 18-month period.

first: T

last: Kosaka

first: H


title: Single-cell RNA-sequencing of metastatic pancreatic neuroendocrine tumor

city: Guangzhou

first: Yu

last: Zhou

state: Guangdong

address: No. 106, Zhognshan Er Road

department: General Surgery

institute: Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences

summary: We report the application of single-cell RNA sequencing (scRNA-seq) technology for single-cell level profiling of the transcriptional features of cells from two primary lesions, one liver metastasis, one normal liver tissue, and peripheral blood monocuclear cells in a patient with metastatic pNET. The transcriptomic profiles of a total of 24.544 cells were captured.

overall_design: Single-cell RNA-sequencing of two primery tumors, one metastatic tumor, one normal liver tissue, and peripheral blood mononuclear cells from one pancreatic neuroendocrine tumor patient with liver metastasis


title: Expression data from human A549 cells with or without circRNA-FOXO3 overexpression

city: Dalian

first: Lizhi

last: Bai

state: Liaoning

address: 6 Jiefang Road, Zhongshan

institute: Affiliated Zhongshan Hospital of Dalian University

summary: To reveal the changes of miRNAs in A549 cells transfected with circRNA-FOXO3, we have employed miRNA microarray expression profiling.

overall_design: circRNA-FOXO3 overexpression induced miRNAs expression in A549 cells was measured .Four independent experiments were performed at each group.


title: Transcriptome analysis of HaCat cells after treatment with siRNA knockdown of Agrin

status: Public on Aug 23 2021

city: Singapore

first: Pierre-alexis

last: Goy

state: Singapore

address: 60 Biopolis Street

country: Singapore

institute: Genome Institute of Singapore (GIS-ASTAR)

summary: This work describes the alteration in the expression of genes in response to siRNA knockdown of Agrin.

overall_design: This dataset contains RNA-seq analysis of siRNA control and siRNA Agrin knockdown cells, taken as triplicates.

first: Sayan

last: Chakraborty

first: Pierre-Alexis


title: Bromodomain containing 9 (BRD9) regulates macrophage inflammatory responses and modulates glucocorticoids receptor activity [CUT&RUN]

city: SCOTTSDALE

first: Zong

last: Wei

address: 13400 E Shea Blvd

institute: Mayo Clinic

summary: In macrophages, homeostatic and immune signals induce distinct sets of transcriptional responses, defining the cellular identity and function. The activity of lineage specific and signal induced transcription factors are regulated by chromatin accessibility and other epigenetic modulators. Glucocorticoids are potent anti-inflammatory drugs. Acting through the glucocorticoid receptor (GR), glucocorticoids directly repress inflammatory responses at transcriptional and epigenetic levels in macrophages. In this study, we identified bromodomain containing 9 (BRD9), a component of SWI/SNF chromatin remodeling complex, as a novel modulator for glucocorticoids responses in macrophages. Inhibition, degradation, or genetic depletion of BRD9 in bone marrow derived macrophages (BMDM), significantly compromised their responses to inflammatory stimuli, such as liposaccharides (LPS), and interferons. A large portion of BRD9-regulated genes are also known to be regulated by dexamethasone, a synthetic glucocorticoid. Importantly, pharmacologic inhibition of BRD9 is able to further potentiate the anti-inflammatory responses of dexamethasone, by further repressing the GR downstream targets. Mechanistically, BRD9 co-localized with a subset of GR binding sites. Depletion of BRD9 enhanced GR occupancy at a subset of its targets. Enhanced occupancy of GR at these sites is associated with further repression of inflammation-related genes. Collectively, these findings establish BRD9 as a key modulator of macrophage inflammatory responses, revealing the therapeutic potential of BRD9 inhibitors as modulators for glucocorticoids action.

overall_design: CUT&RUN sequencing was used to assess BRD9 distribution in RAW264.7 cells.

first: Liu

first: Gabriela

last: Estepa

first: Tae

last: Ohb

first: Jason

last: Magida

first: S

last: Obayomi

first: Ling

last: Chong

first: Diana

last: Hargreaves

first: Ruth

middle: T

last: Yu

first: Annette

middle: R

last: Atkins

first: Michael

last: Downes

first: Ronald

last: Evans


title: Bromodomain containing 9 (BRD9) regulates macrophage inflammatory responses and modulates glucocorticoids receptor activity [RNA-seq]

overall_design: RNA-seq of primary bone marrow-derived macrophages (BMDMs).

last: Wang

middle: M


title: AKIRIN2 controls the nuclear import  of proteasomes in vertebrates

city: Vienna

first: Tobias

last: Neumann

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP

summary: Protein expression and turnover are controlled through a complex interplay of transcriptional, post-transcriptional and post-translational mechanisms to enable spatial and temporal regulation of cellular processes. To systematically elucidate such gene regulatory networks, we developed a CRISPR screening assay based on time-controlled Cas9 mutagenesis, intracellular immunostaining and fluorescence-activated cell sorting that enables the identification of regulatory factors independent of their effects on cellular fitness. We pioneered this approach by systematically probing the regulation of the transcription factor MYC, a master regulator of cell growth. Our screens uncover a highly conserved protein, AKIRIN2, that is essentially required for nuclear protein degradation. We found that AKIRIN2 forms homodimers that directly bind to fully assembled 20S proteasomes to mediate their nuclear import. During mitosis, proteasomes are excluded from condensing chromatin and re-imported into newly formed daughter nuclei in a highly dynamic, AKIRIN2-dependent process. Cells undergoing mitosis in the absence of AKIRIN2 become devoid of nuclear proteasomes, rapidly causing accumulation of MYC and other nuclear proteins. Collectively, our study reveals a dedicated pathway controlling the nuclear import of proteasomes in vertebrates and establishes a scalable approach to decipher regulators in essential cellular processes.

overall_design: mRNA-seq profiles of RKO cells after dox-inducible knockout of AAVS1 (control), AKIRIN2 or the 20S core proteasome subunit PSMA3.

first: Melanie

last: de Almeida

first: Matthias

last: Hinterndorfer

first: Hanna

last: Brunner

first: Irina

last: Grishkovskaya

first: Kashish

last: Singh

first: Alexander

last: Schleiffer

first: Julian

last: Jude

first: Sumit

last: Deswal

first: Robert

last: Kalis

first: Milica

last: Vunjak

first: Thomas

last: Lendl

first: Richard

last: Imre

first: Elisabeth

last: Roitinger

first: Susanne

last: Kadolf

last: Schutzbier

first: Karl

last: Mechtler

first: Gijs

last: Versteeg

first: David

last: Haselbach

first: Johannes

last: Zuber


title: Pharmacological inhibition of CDK4/6 augments long-term anti-tumor immunity through the induction of T cell memory [6_ATACseq_in_vitro_mouse]

city: Melbourne

first: Emily

last: Lelliott

address: 305 Grattan Street

institute: Peter MacCallum Cancer Centre

summary: Small molecule inhibitors of cyclin dependent kinases 4 and 6 (CDK4/6) are an approved treatment for hormone receptor-positive breast cancer and are currently under evaluation across hundreds of clinical trials for other cancer types. The clinical success of these inhibitors is largely attributed to well-defined tumor-intrinsic cytostatic mechanisms, while their emerging role as immunomodulatory agents is less understood. Using integrated epigenomic, transcriptomic and proteomic analyses, we demonstrated a novel action of CDK4/6 inhibitors in promoting the phenotypic and functional acquisition of immunological T cell memory. Short-term priming with a CDK4/6 inhibitor promoted long-term endogenous anti-tumor T cell immunity in mice,  enhanced the persistence and therapeutic efficacy of chimeric antigen receptor (CAR)-T cells, and induced an RB-dependent T cell phenotype supportive of favorable responses to immune checkpoint blockade in melanoma patients. Taken together, these mechanistic insights significantly broaden the prospective utility of CDK4/6 inhibitors as clinical tools to boost anti-tumor T cell immunity.

overall_design: ATAC sequencing of OT-I CD8+ T cells peptide-activated in vitro for 72h, washed and cultured for a further 24h + DMSO/palbociclib in triplicate

first: Stephin

middle: J

last: Vervoort

first: Conor

last: Kearney

first: Karen

last: Sheppard


title: Bromodomain containing 9 (BRD9) regulates macrophage inflammatory responses and modulates glucocorticoids receptor activity [ChIP-seq]

first: Zong

last: Wei

overall_design: We profiled changes of glucocorticoid receptor (GR) in Raw264.7 cells after challenge with Dex+LPS or Dex+LPS+dBRD9.

first: Liu

last: Wang

first: Gabriela

last: Estepa

first: Tae

last: Ohb

first: Jason

last: Magida

first: S

last: Obayomi

first: Ling

last: Chong

first: Diana

last: Hargreaves

first: Ruth

last: Yu

first: Annette

last: Atkins

first: Michael

last: Downes

first: Ronald

last: Evans


title: Dysregulation of TFH-B-TRM lymphocyte cooperation is associated with unfavorable anti-PD-1 responses in EGFR-mutant lung cancer

city: Boston

first: JAE WON

last: CHO

state: MA

address: 60 Fenwood Road

department: Neurology

institute: Brigham and Women's Hospital

summary: Patients with non-small cell lung cancer (NSCLC) with epidermal growth factor receptor (EGFR) mutations exhibit an unfavorable response to PD-1 inhibitor through unclear mechanisms. Hypothesizing that EGFR mutations alter tumor-immune interactions, we compared tumor-infiltrating lymphocytes between EGFR mutant (EGFR-MT) and wild type (EGFR-WT) tumors through single-cell transcriptomic analysis. We found that B cells, CXCL13-producing follicular helper CD4+ T (TFH)-like cells, and tissue-resident memory CD8+ T (TRM)-like cells decreased in EGFR-MT tumors. The NOTCH-RBPJ regulatory network, which is vital for persistence of TRM state, was perturbed, and the interactions between TFH and B cells through the CXCL13-CXCR5 axis disappeared in EGFR-MT tumors. Notably, the proportion of TRM-like cells is predictive for anti-PD-1 response in NSCLC. Our findings suggest that the impairment of TFH-B-TRM cooperation in tertiary lymphoid structure formation, accompanied by the dysregulation of TRM homeostasis and the loss of TFH-B crosstalk, underlies unfavorable anti-PD-1 response in EGFR-MT lung tumors.

overall_design: EGFR wildtype NSCLC patient:5, EGFR mutant NSCLC patient:5

first: Jae-Won

last: Cho

first: Seyeon

last: Park

first: Ga

last: Kim

first: Heonjong

last: Han

first: Hyo

middle: S

last: Shim

first: Sunhye

last: Shin

first: Yong-Soo

last: Bae

first: Seong

first: Sang-Jun

last: Ha

first: Insuk

last: Lee

first: Hye


title: Mapping cell structure across scales by fusing protein images and interactions

city: La Jolla

first: Yue

last: Qin

state: CA

address: 9500 Gilman Drive

institute: University of California San Diego

summary: Enhanced crosslinking and immunoprecipitation assay  (eCLIP) for C-terminally FLAG-HA-tagged RPS3A in HEK293T cells.

overall_design: eCLIP-seq; 2 replicates

first: Maya

middle: L

last: Gosztyla

first: Gene

last: Yeo

first: Trey

last: Ideker


title: Spatially confined sub-tumor microenvironments orchestrate pancreatic cancer pathobiology

city: Toronto

first: Curtis

middle: William

last: McCloskey

state: ON

address: 101 College Street, PMCRT, Room 13-303

department: Medical Biophysics

country: Canada

institute: University Health Network

summary: Pancreatic ductal adenocarcinoma (PDAC) remains resistant to most treatments and demonstrates a complex pathobiology. Here, we deconvolute regional heterogeneity in the human PDAC tumor microenvironment (TME), a long-standing obstacle, to define precise stromal contributions to PDAC progression. Large scale integration of histology-guided multiOMICs profiling with clinical data sets and functional in vitro models uncovered two microenvironmental programs in PDAC that were anchored in fibroblast differentiation states. These sub-tumor microenvironments (subTMEs) co-occurred intratumorally and were spatially confined, producing patient-specific cellular and molecular heterogeneity associated with shortened patient survival. Each subTME was uniquely structured to support discrete aspects of tumor biology: reactive regions rich in activated fibroblast communities were immune-hot and promoted aggressive tumor progression while deserted regions enriched in extracellular matrix supported tumor differentiation yet were markedly chemoprotective. In conclusion, PDAC regional heterogeneity derives from biologically distinct reactive and protective TME elements with a defined, active role in PDAC progression.

overall_design: Single-cell RNA sequencing of  primary PDAC CAF cultures Multiplexed using lipid-tagged indices (MULTI-seq)

first: Barbara

last: Grünwald

first: Rama

last: Khokha


title: Identification of Rac guanine nucleotide exchange factors promoting Lgl1 phosphorylation in glioblastoma

city: Ottawa

first: David

last: Cook

address: 501 Smyth Rd

department: Cancer Therapeutics Program

institute: Ottawa Hospital Research Institute

summary: The protein Lgl has key roles in the regulation of cell polarity. We have shown that Lgl is inactivated by hyperphosphorylation in glioblastoma as a consequence of PTEN loss and aberrant activation of the PI 3-kinase pathway; this contributes to glioblastoma pathogenesis both by promoting invasion and repressing glioblastoma cell differentiation. Lgl is phosphorylated by atypical protein kinase C in a complex with Par6 and either activated Cdc42 or activated Rac. Here we have investigated the role of specific Rac guanine nucleotide exchange factors in Lgl hyperphosphorylation in glioblastoma. We used CRISPR/Cas9 to knockout PREX1, a PI 3-kinase pathway-responsive Rac guanine nucleotide exchange factor that is overexpressed in glioblastoma. Knockout of PREX1 in patient-derived glioblastoma cells resulted in a reduction in Lgl phosphorylation and this could be reversed by re-expressing PREX1. PREX1 knockout cells showed reduced motility and altered phenotype suggestive of partial neuronal differentiation; consistent with this, RNA-seq analyses of these cells identified sets of PREX1-regulated genes with roles in promoting cell motility and repressing neuronal differentiation. Knockout of PREX1 in glioblastoma cells derived from a second patient did not affect Lgl phosphorylation. These cells overexpressed a short isoform of the Rac guanine nucleotide exchange factor TIAM1; knockdown of TIAM1 in PREX1-knockout cells from this patient reduced Lgl phosphorylation. These data show that PREX1 links aberrant PI 3-kinase to Lgl phosphorylation in glioblastoma, but that TIAM1 can also promote Lgl phosphorylation in a subset of patients. While this shows redundant mechanisms for Lgl phosphorylation, PREX1 appears to have a non-redundant role in glioblastoma cell motility, as this was impaired in PREX1 knockout cells from both patients.

overall_design: RNA-seq of PriGO8A human glioblastoma cells following CRISPR-mediated deletion of PREX1 and its doxycycline-inducible restoration. Samples were run in duplicate.

first: Sylvie

last: Lavictoire

first: Danny

last: Jomma

first: Alexander

last: Gont

first: Karen

last: Jardine

first: Ian

middle: A

last: Lorimer


title: Genome resequencing data of adaptive laboratory evolved E. coli W

city: Seoul

first: Sang Woo

last: Seo

address: 1, Gwanak-ro, Gwanak-gu

institute: Seoul National University

summary: Using a synthetic biosensor to couple production of a specific metabolite with cell growth, we spontaneously evolved cells under the selective condition toward the acquisition of genotypes that optimally reallocated cellular resources. Using 3-hydroxypropionic acid (3-HP) production from glycerol in Escherichia coli as a model system, we found spontaneous mutations in the conserved regions of AC and CRP.

overall_design: Comparison of genomic DNA between parental and evolved E. coli W strain

first: Joo

last: Seok

first: Yong

middle: H

last: Han

first: Sang

first: Gyoo

last: Jung


title: Selective molecular responses of rat white adipose tissue according to the fasting stage

city: Strasbourg

first: Fabrice

last: Bertile

address: 25 rue Becquerel

department: Analytical Sciences

institute: CNRS, IPHC

summary:
Prolonged fasting-induced changes in rat white adipose tissue (epidydimal) transcriptome
White adipose tissue is a central place to energy storage and a major endocrine organ. However, adipose molecular mechanisms have been poorly studied during prolonged fasting. To fill this gap, the aim of this study was to decipher transcriptomic regulations in rat adipose tissue during phase 2 (lipid mobilization) and phase 3 (protein catabolism) of prolonged fasting compared to the fed state. We describe a regulatory transcriptional program in epididymal adipose tissue in line with lipogenesis repression during both phases, and that would favor lipolysis during phase 2 and repress it during phase 3. Such regulations notably involve selective (i.e. phase-dependent) changes in gene expression levels of lipases, lipid droplet-associated factors, and the proteins involved in cAMP-dependent and cAMP-independent regulation of lipolysis. The mRNA levels of adipose-secreted factors were globally consistent with the repression of insulin signalling during prolonged fasting. Regulations of leptin and adiponectin levels could be related to their respective role in triggering refeeding during late fasting and controlling lipid metabolism. Specific responses reflecting adipose tissue inflammation, increased fibrinolysis and a possible protein catabolism-related energy saving mechanism were also recorded during phase 3. These data thus provide a comprehensive molecular basis of adipose tissue responses according to the fasting stage.

overall_design: We analyzed epididymal white adipose tissue (epiWAT) from 12 male Sprague Dawley rats randomly divided into 3 groups (4 fed, 4 fasted until phase 2 of fasting [P2], and 4 fasted until phase 3 of fasting [P3]) using the Affymetrix Rat Gene 1.0 ST platform. Array data was processed by Affymetrix GCOS v1.4 and Expression Console v1.1. No techinical replicates were performed.

first: Marianne

last: Ibrahim

first: Daniel

last: Ayoub

first: Thierry

last: Wasselin

first: Alain

last: Van Dorsselaer

first: Yvon

last: Le Maho

last: Raclot


title: Transcriptomic data of CRP(T168P) and AC(S254R) mutant strain of E. coli W

summary: Using a synthetic biosensor to couple production of a specific metabolite with cell growth, we spontaneously evolved cells under the selective condition toward the acquisition of genotypes that optimally reallocated cellular resources. Using 3-hydroxypropionic acid (3-HP) production from glycerol in Escherichia coli as a model system, we determined that spontaneous mutations in the conserved regions of proteins involved in global transcriptional regulation altered the expression of several genes associated with central carbon metabolism. Our study provides a new perspective on adaptive laboratory evolution (ALE) using synthetic biosensors, thereby supporting future efforts in metabolic pathway optimization.

overall_design: mRNA profiles of wild-type (WT) and CRP(T168P) or AC(S254R) mutant strain of E. coli W


title: Genome-wide maps of CRP(T168P)-binding change in Escherichia coli W

overall_design: 8X myc tag was added at the 3' end of wild-type CRP and CRP(T168P) mutant and used for enhanced Chromatin Immunoprecipitation profiling with exonuclease (ChIP-exo).


title: RNA-sequence on kidneys of wild type C57BL/6J and ARLmon/Y mice that underwent orchidectomy and testosterone (or vehicle) replacement for 4 days

city: Heverlee

first: Sarah

last: El Kharraz

address: Herestraat 49

country: Belgium

institute: KU Leuven

summary: We generated a mouse model (ARLmon/Y) with disrupted dimerization of the ligand-binding domain 25 (LBD) of the androgen receptor (AR). These mice exhibit an external female phenotype with undescended testes. Histological analysis of the testes of ARLmon/Y mice revealed some residual spermatogenesis. Hormone measurements in serum of the ARLmon/Y mice showed significantly high levels of androgens. To study if there is any remaining AR activity, we orchidectomized WT and ARLmon/Y mice and gave them supraphysiological testosterone replacement for 4 days. RNA-seq was performed on kindeys.

overall_design: 5 samples per group: WT + Vehicle, WT + testosterone, ARLmon/Y + Vehicle, ARLmon/Y + testosterone

first: Frank

last: Claessens


title: CRP(T168P) and AC(S254R) mutant strain of E. coli W

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Use of Human Adult Stem Cell-Derived Organoid Cultures to Model Enterohepatic Circulation [Ileal organoids]

status: Public on Aug 21 2021

city: Houston

first: Mary

last: Estes

state: TX

address: 1 Baylor Plaza

department: Microbiology and Virology

institute: Baylor College of Medicine

summary: Organ to organ interactions have not yet been modeled with human organoid cultures. This work demonstrates the coupling of intestinal and liver organoids recapitulates aspects of enterohepatic bile signaling. The integration of organoids can be used to probe intra-organ interactions. Total RNA-Seq studies were performed in human ileal organoids to examine expression of bile acid signaling molecules.

overall_design: Ileal organoids from two independent individuals were used for total RNA sequencing.

middle: E

last: Blutt

first: Sue

last: Crawford

first: Sasirekha

last: Ramani

first: Xi-Lei

last: Zeng

first: Matthew

last: Robertson

first: Hoa

last: Nguyen-Phuc

first: Cristian

last: Coarfa

middle: K


title: The PLCP gene family of grapevine (Vitis vinifera L.) : Characterization and differential expression in response to Plasmopara Viticola

status: Public on Aug 22 2021

city: Nanjing

first: Peijie

last: Gong

address: Weigang Nr.1

institute: Nanjing Agricultural University

summary: In order to investigate the putative roles of the VvPLCP genes in grapevine resistance, the leaves-specific expression patterns of VvPLCPs were analyzed according to transcriptome data in two cultivars including V. vinifera cv. ‘Zitian Seedless’ and Vitis rootstocks ‘Kober 5BB’ when infected with P. viticola

overall_design: Expression data for VvPLCP genes was obtained from this transcriptome data. The expression levels of V. vinifera cv.‘Zitian Seedless’and Vitis rootstocks‘Kober 5BB’leaves at 0, 24, and 72 h after P. viticola BS-4-MW infection

first: Jun

last: Kang

first: Mengqing

last: Ge

first: Sadeghnezhad

last: Ehsan


title: Programmatic Introduction of Parenchymal Cell Types in Blood Vessel Organoids

status: Public on Aug 20 2021

first: Udit

last: Parekh

address: 9500 Gilman Drive, Room 353, Powell-Focht (EBU3A)

department: Bioengineering

institute: University of California, San Diego

summary: We developed a bottom-up engineering approach to building vascularized human tissue by combining genetic reprogramming with chemically directed organoid differentiation. As a proof of concept, we created neuro-vascular and myo-vascular organoids via transcription factor overexpression in vascular organoids. We characterized neuro-vascular organoids (iN-VOs) by single cell RNA-sequencing (scRNA-seq) to determine cell type composition and gene expression. Using droplet based scRNA-seq we analyzed over 26,000 cells across day 45 organoids grown under three conditions: 45 days of NEUROD1 overexpression (iN-VO, 45 Days Induction), 15 days of NEUROD1 overexpression (iN-VO, 15 Days Induction) and without overexpression (iN-VO, No Induction). We find that organoids contain a neural cell population only upon induction of NEUROD1 while maintaining the full set of endothelial and mesenchymal lineages present in uninduced vascular organoids.

overall_design: Single cell RNA-Seq for blood vessel organoids with 45 days, 15 days and no NEUROD1 induction

first: Amir

last: Dailamy

first: Dhruva

last: Katrekar

first: Aditya

last: Kumar

first: Daniella

last: McDonald

first: Ana

last: Moreno

first: Pegah

last: Bagheri

first: Tse

last: Ng

first: Prashant

last: Mali


title: RNA-sequence on testes of wild type C57BL/6J, ARLmon/Y and AR-/Y mice

first: Sarah

last: El Kharraz

summary: We generated a mouse model (ARLmon/Y) with disrupted dimerization of the ligand-binding domain 25 (LBD) of the androgen receptor (AR). These mice exhibit an external female phenotype with undescended testes. Histological analysis of the testes of ARLmon/Y mice revealed some residual spermatogenesis. Hormone measurements in serum of the ARLmon/Y mice showed significantly high levels of androgens. To further explore the ARLmon/Y testicular phenotype, we performed RNA-sequencing on while testis of five mice per genotype.

overall_design: 5 samples per genotype: wild type C57BL/6J, ARLmon/Y and AR-/Y mice

first: Frank

last: Claessens


title: The Complex Transcriptional Architecture of Magnetosome Operons in Magnetospirillum gryphiswaldense

city: Bayreuth

first: Cornelius

middle: Nicolas

last: Riese

address: Universitätsstraße 30

department: Microbiology

institute: University of Bayreuth

summary: Magnetosomes are complex membrane organelles synthesized by magnetotactic bacteria (MTB) for navigation in the magnetic field. Their formation is tightly controlled by ˃30 specific magnetosome genes arranged in operons. The transcriptional organization of these operons in the model MTB Magnetospirillum gryphiswaldense MSR-1 has been long viewed to be simple, having each a convenient promoter that enable transcription of the operon as a single transcriptional unit. Here, by applying Cappable-seq and whole transcriptome shotgun RNA sequencing, we revealed multiple additional transcription starting sites (TSS) within the magnetosome operons mamABop, mms6op and mamXYop. Using experimental validation by bioluminescence reporter, we demonstrated that most of the new TSS are generated by biologically meaningful promoters. Furthermore, the knockout of the primary promoters in mamABop and mms6op resulted only in mild impairments of the magnetosome formation, suggesting that additional transcripts are indeed generated within these operons. Besides, we identified a strong promoter in the intergenic region within mamXYop, which transcript likely represents a non-coding RNA important for proper expression of the genes in this operon. The promoter sequences from MSR-1 are conservative in most magnetotactic Magnetospirillum spp., but not in other MTB, suggesting the functional conservation in magnetospirilla but independent evolution of the transcription circuits within the magnetosome operons in different phylogenetic groups. Taken together, our data suggest much more complex transcriptional architecture of the magnetosome operons in MSR-1 than deemed before and contribute to unraveling the fundamentals of magnetosome biosynthesis at transcriptional level.

overall_design: RNA-Seq of primary transcripts, whole transcriptome and 3'-ends of wild type cells

first: Marina

last: Dziuba

first: Manuel

last: Wittchen

first: Tobias

last: Busche

first: Jörn

last: Kalinowsky

first: Dirk

last: Schüler


title: Regulation of intestinal immunity and tissue repair by enteric glia   (Single-cell expression analysis of tunica muscularis cells from naïve and H. poly-infected Ifngr2CTRL and Ifngr2ΔEGC mice.)

city: London

first: Brigitta

last: Stockinger

address: 1 Midland Road

institute: The Francis Crick Institute

summary: Tissue maintenance and repair depend on the integrated activity of multiple cell types. Whereas the contributions of epithelial, immune and stromal cells in intestinal tissue integrity are well understood, the role of intrinsic neuroglia networks remains largely unknown. Here, we uncover pivotal roles of enteric glial cells (EGCs) in intestinal homeostasis, immunity and tissue repair. We demonstrate that infection of mice with Heligmosomoides polygyrus (H. poly) leads to enteric gliosis and upregulation of the interferon gamma (IFN-γ) gene signature. Single-cell transcriptomics of tunica muscularis (TM) showed that glia-specific abrogation of IFN-γ signaling leads to tissue-wide activation of pro-inflammatory transcriptional programs. In addition, disruption of the IFN-γ-EGC signaling axis enhanced the inflammatory and granulomatous response of TM to helminths. Mechanistically, we show that upregulation of Cxcl10 is an early immediate response of EGCs to IFN-γ signaling and provide evidence that this chemokine and the downstream amplification of IFN-γ signaling in the TM are required for a measured inflammatory response to helminths and resolution of granulomatous pathology. Our study demonstrates that IFN-γ signaling in enteric glia is central to intestinal homeostasis and reveals critical roles of the IFN-γ-EGC-Cxcl10 axis in immune response and tissue repair following infectious challenge.  To understand mechanistically how the IFN-γ-EGC axis regulates the intestinal response to helminth infection, we used scRNAseq analysis of the TM as an unbiased means to identify tissue-wide changes in cellular composition and gene expression associated with glia-specific abrogation of IFN-γ signalling.

overall_design: To understand the homeostatic roles of the IFN-γ-EGC signalling axis on the TM and to examine the role of the IFN-γ-EGC signalling axis in the response of host tissue to helminths, we compared the cellular and transcriptional landscape of the TM from naive and H. poly-infected Ifngr2CTRL (Sox10-CreERT2;Ifngr2+/fl, Ifngr2tm1.1Lflu, MGI: 6402706 15) and Ifngr2ΔEGC (Sox10-CreERT2;Ifngr2fl/fl) mice. We isolated cells from two experimental replicates (1: one mouse per sample, 2: a pool of three mice per sample) for each condition (naïve Ifngr2CTRL, naïve Ifngr2ΔEGC, 7 days of H. poly infection Ifngr2CTRL, 7 days of H. poly infection Ifngr2 ΔEGC) from both males and females at 10 days after tamoxifen induction.

first: Fränze

last: Progatzky

first: Michael

last: Shapiro

first: Song

last: Chng

first: Bethania

last: Garcia-Cassani

first: Cajsa

last: Classon

first: Selin

last: Sevgi

first: Anna

last: Laddach

middle: C

last: Bon-Frauches

first: Reena

last: Lasrado

first: Maryam

last: Rahim

first: Eleni-Maria

last: Amaniti

first: Stefan

last: Boeing

first: Kathleen

last: Shah

first: Lewis

last: Entwistle

first: Alejandro

last: Suárez-Bonnet

first: Mark

last: Wilson

first: Vassilis

last: Pachnis


title: Expression profiling of lung endothelial cells during metastatic progression. [RNA-Seq]

city: Mannheim

first: Mahak

last: Singhal

address: Ludolf-Krehl-Straße 13-17

institute: European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University

summary: Lung EC were isolated at sequential stages of tumor progression and bulk RNA-seq analysis was performed.

overall_design: Total RNA-sequencing FACS-sorted lung endothelial cells was undertaken. Four independent biological replicates for each timepoint were analysed.

first: Hellmut

middle: G

last: Augustin


title: Expression profiling of lung pericytes treated with conditioned media from tumor cells

summary: Lung pericytes treated with tumor-CM were processed and bulk RNA-seq analysis was performed.

overall_design: Total RNA-sequencing of lung pericytes was undertaken. Four independent biological replicates for each biological group were analysed.


title: Integrating whole blood transcriptomic collection procedures into the current anti-doping testing system, including long-term storage and re-testing of anti-doping samples [Long-term]

status: Public on Sep 03 2021

city: Rome

first: Giscard

middle: Humberto Oliveira

last: Lima

address: Piazza Lauro de Bosis, 15

country: Italy

institute: University of Rome Foro Italico

summary:
Purpose: Recombinant human erythropoietin administration studies involving “omics” approaches have demonstrated a gene-expression signature that could aid detection of blood doping. However, current anti-doping testing does not involve blood collection into tubes with RNA preservative. This study investigated if whole blood in long-term storage could be used for transcriptomic analysis despite lacking RNA preservation.
Methods: Whole blood samples were collected from thirteen male healthy individuals. Long-term storage: whole blood collected into Tempus™ tubes and K2EDTA tubes and subjected to long-term (i.e., −80°C) storage and RNA extracted. After storage, Tempus and K2EDTA tubes were thawed and extracted using Tempus™ Spin RNA Isolation Kit (Life Technologies, Carlsbad, CA, USA). Samples from seven subjects that presented higher RIN value (≥7) were selected for RNA_Seq analysis.
Results: The experiment provided RNA quality and purity for gene expression analysis. Total of 19239 genes were mapped and the gene expression analysis showed that 658 genes were differentially expressed (which means 3.4% of mapped genes). With 269 being up-regulated and 389 down-regulated. None of the transcripts described in previous studies as biomarkers for blood doping (Durussel et al. 2016; Wang, Durussel, et al. 2017) were differently expressed.
Conclusion: RNA quantity, purity and integrity was not significantly compromised from long-term storage in blood storage tubes lacking RNA stabilisation, indicating that transcriptomic/omics analysis could be conducted using anti-doping samples collected or biobanked without RNA preservation.

overall_design: Blood samples were collected using K2EDTA tubes or Tempus (control). After long-term storage, blood samples from K2EDTA tubes were transferred into Tempus tube. Both groups (EDTA+Tempus and Tempus) were extracted by using Tempus™ Spin RNA Isolation Kit. The different gene expression between groups was compared.

first: Alexander

last: Kolliari-Turner

first: Fernanda

last: Malinsky

first: Fergus

last: Guppy

first: Renan

middle: P

last: Martin

first: Guan

last: Wang

first: Sven

last: Voss

first: Costas

last: Georgakopoulos

first: Paolo

last: Borrione

first: Fabio

last: Pigozzi

first: Yannis

last: Pitsiladis


title: Expression profiling of lung endothelial cells during metastatic progression.


title: Induced muscle progenitor cells

first: Fei

last: Ji

address: 185 Cambridge St

institute: Massachusetts General Hospital


title: Gene-expression analysis of chilblain-like lesion during COVID-19 pandemic compared to seasonal chilblain

status: Public on Aug 19 2021

city: Paris

first: Charles

last: Cassius

address: 1 avenue Claude Vellefaux

department: Dermatologie

institute: Hôpital Saint-Louis

summary: The aim of this study was to assess the gene expression profil of skin chilblain-like lesions that appeared during the COVID-19 pandemic and to compare it with seasonal chilblain and healthy skin

overall_design: 18 samples were included, 10 chilblain-like lesion, 4 seasonal chilblain and 4 healthy skin

first: Laure

last: Fumholtz

first: Jean-David

last: Bouaziz

first: Maxime

last: Battistella

first: Jerome

last: Hadjadj

first: Richard

last: Chocron

first: Dajouida

last: Bengoufa

first: Hélène

last: Le Buanec

first: Laura

last: Barnabei

first: Sonia

last: Meynier

first: Olivier

last: Schwartz

first: Ludivine

last: Grzelak

first: Nikaïa

last: Smith

first: Bruno

last: Charbit

first: Darragh

last: Duffy

first: Nader

last: Yatim

first: Andreea

last: Calugareanu

first: Aurélien

last: Philippe

first: Coralie

last: Guerin

first: Bérangère

last: Joly

first: Virginie

last: Siguret

first: Léa

last: Jaume

first: Hervé

last: Bachelez

first: Martine

last: Bagot

first: Frédéric

last: Rieux-Laucat

first: Sarah

last: Maylin

first: Jérome

last: Legoff

first: Constance

last: Delaugerre

first: Nicolas

last: Gendron

first: David

last: Smadja


title: Therapeutic melanoma inhibition by local micelle-mediated cyclic nucleotide repression

city: Mainz

first: Matthias

last: Klein

address: Langenbeckstrasse 1

department: Inst. for Immunology

institute: University Medical Center Mainz

summary: The acidic tumor microenvironment in melanoma drives immune evasion by up-regulating cyclic adenosine monophosphate (cAMP) in tumor-infiltrating monocytes..Melanoma growth can be suppressed by releasing non-toxic concentrations of an adenylate cyclase (AC) inhibitor from polypept(o)id micelles at the tumor site in an immune cell-dependent manner.

overall_design:
Whole transcriptome analysis (WTA) of CD45+ single cells from Nanoparticle (polypept(o)id micelles)-treated day 15 B16F10-OVA Tumors of B6 mice. Particles were peritumorally injected at the tumor site every other day starting at day 4 after tumor inoculation. Mice either received empty particles (NL-PM) or MDL-12.330A-loaded Particles (L-PM) (n=3 animals/experimental group)

The linked python script (in the tar archive at the foot of this record) can be used to translate cell indexes to raw sequences found in the fastq files. See the linked readme file for further instructions.

first: Toszka

last: Bohn

first: Fatemeh

last: Shahneh

first: Tobias

last: Bopp

first: Christian

last: Becker


title: RNA sequencing of particulate metter treated melanocytes

first: Sang Ho

last: Oh

address: 50-1 Yonsei-ro

department: Dermatology

institute: Yonsei University College of Medicine

summary: Purpose: Determine the mechanism of particulate matter-induced signaling in melanocytes.  Method: Primary human epidermal melanocytes were treated with particulate matter (5 μg/cm2) and incubated for 24 h. Total RNA (1 ug) from melanocytes were extracted and subjected to library synthesis.   Results: Particulate matter-treated melanocytes exhibited upregulation of ER stress, unfolded protein response, and melanogenesis-related molecules.   Conclusion: Particulate matter-induced melanocyte signaling was well evaluated using RNA sequencing.

overall_design: mRNA profiles of particulate matter treated human melanocyte

first: Sang

first: Yuri

last: Ahn

first: Eun

last: Lee


title: A cis-acting mechanism mediates trancriptional memory at Polycomb target genes in mammals [WGBS]

first: Daniel

last: Holoch

state: Cedex 05

address: 26 rue d'Ulm

department: Genetics and Developmental Biology Unit

institute: Institut Curie, Centre de Recherche

summary: Epigenetic inheritance of gene expression states enables a single genome to maintain distinct cellular identities. How histone modifications contribute to this process remains unclear. Using global chromatin perturbations and local, time-controlled modulation of transcription, we establish the existence of epigenetic memory of transcriptional activation for genes that can be silenced by the Polycomb group. This property emerges during cell differentiation and allows genes to be stably switched following a transient transcriptional stimulus. This transcriptional memory state at Polycomb targets operates in cis; however, rather than relying solely on read-and-write propagation of histone modifications, the memory is also linked to the strength of activating input opposing Polycomb proteins and therefore varies with the cellular context. Our data and computational simulations suggest a model whereby transcriptional memory arises from double-negative feedback between Polycomb-mediated silencing and active transcription. Epigenetic memory at Polycomb targets thus depends not only on histone modifications but also on the gene-regulatory network and underlying identity of a cell.

overall_design: 5-methylcytosine profiling (WGBS) of immortalized mouse embryonic fibroblast line A (= C2) in wild-type (2 replicates), Ezh2 KO (2 replicates) conditions (4 samples).

first: Michel

last: Wassef

first: Cecilia

last: Lövkvist

first: Dina

last: Zielinski

first: Setareh

last: Aflaki

first: Bérangère

last: Lombard

first: Tiphaine

last: Héry

first: Damarys

last: Loew

first: Martin

last: Howard

first: Raphaël

last: Margueron


title: A cis-acting mechanism mediates trancriptional memory at Polycomb target genes in mammals [ATAC-seq]

overall_design: Chromatin accessibility profiles (ATAC-seq) of immortalized mouse embryonic fibroblast line A (= C2) in wild-type (2 replicates), Ezh2 KO (2 replicates) and Ezh2 rescue (2 replicates) conditions (6 samples).


title: Identification of key regulatory pathways in response to long-term zinc supplementation in human primary retinal pigment epithelium: a multi-omics approach

city: Belfast

first: Imre

last: Lengyel

state: English

address: 97 Lisburn Road, Centre for Experimental Medicine, Queens Un

institute: Queens University Belfast

summary:
Purpose: In age-related macular degeneration (AMD), both systemic and local zinc concentrations are decreased. Elevating zinc levels by nutrition or oral supplementation has a positive impact on delaying the progression to end-stage AMD in clinical studies. Here we set out to identify key regulatory pathways involved in this beneficial effect in retinal pigment epithelial cells.
Methods: Transcriptome profiles of 5 weeks old primary human fetal retinal pigment epithelial cells from 3 different donors were generated by RNA sequencing using Illumina NextSeq 5000. The samples from the 3 donors represent replicates of each conditions. The sequence reads that passed quality filters were analyzed further for differentially expressed genes (DEG) performing quasi-likelihood F-test in edgeR package (Robinson, McCarthy et al. 2010). Lowly expressed genes were filtered out using the following script was used: > keep <- rowSums(cpm(y)> 0.05) >= 1. To be considered as differentislly expressed gene, the Benjamini-Hochberg–adjusted P value was less than 0.05.
Results: Using our data analysis workflow, we were able to identify over 32,000 transcripts. 826 of these were significantly changed in the three independent samples after apical and 218 after basal zinc supplementation when compared to untreated controls. Apical zinc supplementation upregulated 415 and down-regulated 411 transcripts. Basal zinc supplementation upregulated 157 and down-regulated 59 transcripts. 163 transcripts changed similarly after both apical and basal treatment.

overall_design: Transcriptome profile of human primary fetal retinal pigment epithelial cells from 3 donors (n=12) following zinc apical (n=4) or basal (n=3) supplementation compared to untreated cells (n=5)

first: Eszter

last: Emri


title: Genetic and epigenetic orchestration of Gfi1aa-Lsd1-cebpa in zebrafish neutrophil development

city: Guangzhou

first: Mei

last: Wu

address: Waihuan Dong Road

department: School of Medicine

institute: South China University of Technology

summary: Neutrophils are the most abundant vertebrate leukocytes and they are essential to host defense. Despite extensive investigation, the molecular network controlling neutrophil differentiation remains incompletely understood. GFI1 is associated with several myeloid disorders, but its role and the role of its co-regulators in granulopoiesis and pathogenesis are far from clear. Herein, we demonstrate that zebrafish gfi1aa deficiency induces excessive neutrophil progenitor proliferation, accumulation of immature neutrophils from the embryonic stage, and some phenotypes similar to myelodysplasia syndrome in adulthood. Both genetic and epigenetic analysis demonstrated immature neutrophil accumulation in gfi1aa-deficient mutants to be due to up-regulation of cebpα transcription. Increased transcription was associated with Lsd1 altered H3K4 methylation of cebpα regulatory region. Taken together, results demonstrated Gfi1aa, Lsd1, and cebpα to form a regulatory network that controlled neutrophil development, providing a disease progression traceable model for myelodysplasia syndrome. The use of the model will provide new insights into a molecular understanding of GFI1 related myeloid disorders as well a mean by which to develop targeted therapeutic approaches for treatment.

overall_design: Examination of Gfi1aa binding sites in zebrafish embryos

first: Junwei

last: Lian

first: Yiyue

last: Zhang


title: Expression profiling of lung endothelial cells during metastatic progression. [scRNA-Seq]

first: Mahak

last: Singhal

summary: Lung EC were isolated at sequential stages of tumor progression and 10x Genomics-based single-cell RNA-seq analysis was performed.

overall_design: 10000 FACS-sorted lung EC were used for the library preparation. For each sample four libraries were generated. The multiplexd samples were sequenced with a HiSeq 4000 machine.

first: Hellmut

last: Augustin